Lessons learned from protein aggregation: toward technological and biomedical applications

Abstract

The close relationship between protein aggregation and neurodegenerative diseases has been the driving force behind the renewed interest in a field where biophysics, neurobiology and nanotechnology converge in the study of the aggregate state. On one hand, knowledge of the molecular principles that govern the processes of protein aggregation has a direct impact on the design of new drugs for high-incidence pathologies that currently can only be treated palliatively. On the other hand, exploiting the benefits of protein aggregation in the design of new nanomaterials could have a strong impact on biotechnology. Here we review the contributions of our research group on novel neuroprotective strategies developed using a purely biophysical approach. First, we examine how doxycycline, a well-known and innocuous antibiotic, can reshape α-synuclein oligomers into non-toxic high-molecular-weight species with decreased ability to destabilize biological membranes, affect cell viability and form additional toxic species. This mechanism can be exploited to diminish the toxicity of α-synuclein oligomers in Parkinson's disease. Second, we discuss a novel function in proteostasis for extracellular glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in combination with a specific glycosaminoglycan (GAG) present in the extracellular matrix. GAPDH, by changing its quaternary structure from a tetramer to protofibrillar assembly, can kidnap toxic species of α-synuclein, and thereby interfere with the spreading of the disease. Finally, we review a brighter side of protein aggregation, that of exploiting the physicochemical advantages of amyloid aggregates as nanomaterials. For this, we designed a new generation of insoluble biocatalysts based on the binding of photo-immobilized enzymes onto hybrid protein:GAG amyloid nanofibrils. These new nanomaterials can be easily functionalized by attaching different enzymes through dityrosine covalent bonds.

Keywords: Alzheimer’s disease; Amyloid; Amyloid functionalization; Cross-beta structure; Glycosaminoglycan; Parkinson’s disease; Protein aggregation.

Fig. 1

A simplified representation of a protein aggregation pathway: Nascent and intrinsically disordered proteins (IDP) (unfolded, in violet) fold into a native functional state (folded, green), which is thermodynamically favored in globular proteins. Small destabilizing fluctuations in the intracellular medium can shift the equilibrium and increase the population of partly folded molecules. Under normal conditions, these are refolded by molecular chaperones or cleared by the ubiquitin–proteasome machinery (removal for reuse). Should these machineries be impaired or the populations of misfolded molecules overwhelm their buffering possibility, the equilibrium could lean towards amyloid fibrils (blue) or amorphous aggregates (red). The assembly of oligomers (blue) precedes that of amyloid fibrils, which are characterized by a specific X-ray diffraction pattern due to their cross-beta structure (inset). Kinetics data of particle size increase help distinguish between these two forms of aggregates

Fig. 2

Three-dimensional model of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protofibril: a Surface representation of a GAPDH protofibril formed in the presence of heparin. b Top view of the protofibril. The building block is represented as a transparent surface while the β-sheets that might be involved in the formation of cross-β structures in the mature fibril are shown in cartoon representation. c Spatial aggregation propensity mapped onto the protofibril solvent accessible surface. The red regions indicate aggregation prone sites with hydrophobic patches exposed. Adapted from Avila et al. (2014)

Fig. 3

Mechanism of α-synuclein sequestration by GAPDH protofibrils. In the extracellular space, glycosaminoglycans (GAGs) induce GAPDH dissociation into dimers, which then reassemble into high-molecular weight species such as protofibrils. GAPDH protofibrils are able to sequester α-synuclein oligomers into a mixed fibril through the hydrophobic patch present at the edge of the protofibril. Reproduced from Avila et al. (2014)

Fig. 4

a Variable-pressure-scanning electron microscopy image of lysozyme fibrils formed in the presence of heparin. b Time evolution of deconvolved amide I infrared spectra lysozyme incubated with heparin. c Putative model of heparin inducing dimerization of lysozyme in the first step of aggregation. Figures adapted from Chaves et al. (2016)